Starting phenix.real_space_refine on Fri Jul 3 03:08:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fya_29562/07_2026/8fya_29562.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fya_29562/07_2026/8fya_29562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2026/8fya_29562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2026/8fya_29562.map" model { file = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2026/8fya_29562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2026/8fya_29562.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 31 5.16 5 C 7056 2.51 5 N 2060 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11433 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2388 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 1 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Time building chain proxies: 2.15, per 1000 atoms: 0.19 Number of scatterers: 11433 At special positions: 0 Unit cell: (93.66, 90.315, 142.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 57 15.00 O 2229 8.00 N 2060 7.00 C 7056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 272.8 milliseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 51.2% alpha, 15.4% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.823A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.982A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 180 through 205 Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.872A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.343A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.871A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.517A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'C' and resid 180 through 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.722A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.507A pdb=" N LEU C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 3.539A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.999A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.581A pdb=" N ARG E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.806A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.451A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.648A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.881A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 139 through 163 Processing helix chain 'F' and resid 180 through 205 Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.758A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.868A pdb=" N LEU F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.798A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.461A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291 removed outlier: 8.105A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310 removed outlier: 3.901A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.287A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 291 removed outlier: 7.715A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310 removed outlier: 7.598A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3360 1.34 - 1.45: 2039 1.45 - 1.57: 6193 1.57 - 1.69: 114 1.69 - 1.81: 60 Bond restraints: 11766 Sorted by residual: bond pdb=" C3' DT H 9 " pdb=" C2' DT H 9 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT H 30 " pdb=" C2' DT H 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA G 21 " pdb=" C2' DA G 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT H 3 " pdb=" C2' DT H 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC G 17 " pdb=" C2' DC G 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 15468 1.20 - 2.41: 565 2.41 - 3.61: 118 3.61 - 4.81: 12 4.81 - 6.02: 11 Bond angle restraints: 16174 Sorted by residual: angle pdb=" O4' DA G 25 " pdb=" C4' DA G 25 " pdb=" C3' DA G 25 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT H 20 " pdb=" C4 DT H 20 " pdb=" O4 DT H 20 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT H 9 " pdb=" C4 DT H 9 " pdb=" O4 DT H 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 30 " pdb=" C4 DT H 30 " pdb=" O4 DT H 30 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 3 " pdb=" C4 DT H 3 " pdb=" O4 DT H 3 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6645 35.99 - 71.98: 279 71.98 - 107.97: 9 107.97 - 143.96: 0 143.96 - 179.96: 1 Dihedral angle restraints: 6934 sinusoidal: 3177 harmonic: 3757 Sorted by residual: dihedral pdb=" C4' DC G 8 " pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " pdb=" P DT G 9 " ideal model delta sinusoidal sigma weight residual -140.00 39.96 -179.96 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ARG E 34 " pdb=" C ARG E 34 " pdb=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU F 19 " pdb=" C GLU F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1248 0.037 - 0.074: 395 0.074 - 0.110: 142 0.110 - 0.147: 36 0.147 - 0.184: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CB VAL C 191 " pdb=" CA VAL C 191 " pdb=" CG1 VAL C 191 " pdb=" CG2 VAL C 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB THR E 113 " pdb=" CA THR E 113 " pdb=" OG1 THR E 113 " pdb=" CG2 THR E 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1820 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 172 " -0.025 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 173 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 85 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 86 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " -0.009 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR A 31 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.000 2.00e-02 2.50e+03 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 492 2.72 - 3.26: 11148 3.26 - 3.81: 20453 3.81 - 4.35: 25083 4.35 - 4.90: 41575 Nonbonded interactions: 98751 Sorted by model distance: nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR E 229 " pdb=" OD2 ASP E 275 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 7 " pdb=" OG SER A 57 " model vdw 2.201 3.040 nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.207 3.040 nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.213 3.040 ... (remaining 98746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 20 through 283) selection = (chain 'C' and resid 20 through 283) selection = (chain 'F' and resid 20 through 283) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.790 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11766 Z= 0.280 Angle : 0.555 6.016 16174 Z= 0.386 Chirality : 0.043 0.184 1823 Planarity : 0.003 0.047 1879 Dihedral : 16.989 179.956 4524 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 601 sheet: 0.05 (0.40), residues: 201 loop : -0.49 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 124 TYR 0.022 0.001 TYR A 31 PHE 0.008 0.001 PHE A 35 TRP 0.005 0.001 TRP E 83 HIS 0.010 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.28 (11766) covalent geometry : angle 0.55490 / 0.39 (16174) hydrogen bonds : bond 0.16746 / 11.14 ( 621) hydrogen bonds : angle 6.58993 / 4.64 ( 1724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.399 Fit side-chains REVERT: A 58 MET cc_start: 0.8838 (ttp) cc_final: 0.8525 (ttp) REVERT: C 257 LEU cc_start: 0.8442 (tt) cc_final: 0.7867 (tp) REVERT: F 254 LEU cc_start: 0.8295 (tt) cc_final: 0.8082 (tt) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.5224 time to fit residues: 137.4697 Evaluate side-chains 181 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 33 ASN C 308 ASN F 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124309 restraints weight = 12456.092| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.77 r_work: 0.3318 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11766 Z= 0.210 Angle : 0.629 9.073 16174 Z= 0.347 Chirality : 0.046 0.257 1823 Planarity : 0.005 0.040 1879 Dihedral : 18.544 179.598 2097 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.81 % Allowed : 11.82 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.24), residues: 1288 helix: 1.96 (0.21), residues: 607 sheet: -0.22 (0.38), residues: 206 loop : -0.60 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 69 TYR 0.021 0.002 TYR A 31 PHE 0.016 0.002 PHE D 89 TRP 0.010 0.001 TRP B 296 HIS 0.013 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (11766) covalent geometry : angle 0.62882 / 0.35 (16174) hydrogen bonds : bond 0.05591 / 3.82 ( 621) hydrogen bonds : angle 4.78393 / 3.39 ( 1724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.458 Fit side-chains REVERT: A 71 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8333 (mt) REVERT: B 302 LEU cc_start: 0.8345 (mt) cc_final: 0.8073 (mm) REVERT: C 257 LEU cc_start: 0.8339 (tt) cc_final: 0.7963 (tp) REVERT: D 31 TYR cc_start: 0.8519 (m-80) cc_final: 0.8168 (m-80) REVERT: E 31 LYS cc_start: 0.8172 (mtpm) cc_final: 0.7688 (mttp) REVERT: E 244 GLU cc_start: 0.7710 (tt0) cc_final: 0.7373 (tt0) REVERT: E 254 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7734 (tt) REVERT: E 289 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5438 (pp20) outliers start: 30 outliers final: 14 residues processed: 209 average time/residue: 0.5096 time to fit residues: 115.7547 Evaluate side-chains 182 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126600 restraints weight = 12472.147| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.80 r_work: 0.3350 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11766 Z= 0.142 Angle : 0.537 6.793 16174 Z= 0.302 Chirality : 0.042 0.220 1823 Planarity : 0.004 0.036 1879 Dihedral : 18.645 178.918 2097 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.19 % Allowed : 14.54 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1288 helix: 2.14 (0.21), residues: 608 sheet: -0.36 (0.37), residues: 206 loop : -0.53 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 69 TYR 0.009 0.001 TYR F 126 PHE 0.011 0.001 PHE F 263 TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11766) covalent geometry : angle 0.53658 / 0.30 (16174) hydrogen bonds : bond 0.05015 / 3.43 ( 621) hydrogen bonds : angle 4.51472 / 3.20 ( 1724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.410 Fit side-chains REVERT: A 58 MET cc_start: 0.9067 (ttp) cc_final: 0.8694 (ttp) REVERT: B 302 LEU cc_start: 0.8281 (mt) cc_final: 0.8023 (mm) REVERT: C 17 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7571 (mtm-85) REVERT: C 257 LEU cc_start: 0.8256 (tt) cc_final: 0.7937 (tp) REVERT: D 10 ASN cc_start: 0.7342 (t0) cc_final: 0.6996 (m-40) REVERT: D 23 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8592 (ptm) REVERT: E 31 LYS cc_start: 0.8063 (mtpm) cc_final: 0.7594 (mttp) REVERT: E 33 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7523 (m-40) REVERT: E 244 GLU cc_start: 0.7642 (tt0) cc_final: 0.7331 (tt0) REVERT: F 121 VAL cc_start: 0.7895 (t) cc_final: 0.7688 (t) REVERT: F 253 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7906 (tm-30) outliers start: 34 outliers final: 14 residues processed: 207 average time/residue: 0.5339 time to fit residues: 120.3530 Evaluate side-chains 181 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 123 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126154 restraints weight = 12434.836| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.76 r_work: 0.3339 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11766 Z= 0.152 Angle : 0.534 6.726 16174 Z= 0.300 Chirality : 0.042 0.230 1823 Planarity : 0.004 0.033 1879 Dihedral : 18.704 179.649 2095 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.19 % Allowed : 15.20 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.24), residues: 1288 helix: 2.18 (0.21), residues: 610 sheet: -0.43 (0.36), residues: 206 loop : -0.52 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 21 TYR 0.013 0.001 TYR D 31 PHE 0.012 0.001 PHE D 89 TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (11766) covalent geometry : angle 0.53393 / 0.30 (16174) hydrogen bonds : bond 0.04781 / 3.30 ( 621) hydrogen bonds : angle 4.38729 / 3.12 ( 1724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9080 (ttp) cc_final: 0.8685 (ttp) REVERT: B 302 LEU cc_start: 0.8382 (mt) cc_final: 0.8140 (mm) REVERT: C 17 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7615 (mtm-85) REVERT: C 232 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7541 (pp20) REVERT: C 257 LEU cc_start: 0.8259 (tt) cc_final: 0.7959 (tp) REVERT: D 23 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8559 (ptm) REVERT: E 33 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7558 (m-40) REVERT: E 244 GLU cc_start: 0.7634 (tt0) cc_final: 0.7343 (tt0) REVERT: E 270 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7594 (mtpt) REVERT: E 271 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7502 (mtm110) REVERT: E 289 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5428 (pp20) REVERT: F 121 VAL cc_start: 0.7982 (t) cc_final: 0.7760 (t) REVERT: F 138 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6104 (tt) outliers start: 34 outliers final: 17 residues processed: 196 average time/residue: 0.4815 time to fit residues: 102.4920 Evaluate side-chains 195 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125883 restraints weight = 12469.462| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.79 r_work: 0.3329 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11766 Z= 0.152 Angle : 0.531 6.547 16174 Z= 0.296 Chirality : 0.042 0.229 1823 Planarity : 0.004 0.046 1879 Dihedral : 18.820 179.545 2095 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.85 % Allowed : 15.48 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1288 helix: 2.22 (0.21), residues: 609 sheet: -0.47 (0.36), residues: 206 loop : -0.49 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.009 0.001 TYR E 229 PHE 0.013 0.001 PHE F 263 TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (11766) covalent geometry : angle 0.53080 / 0.30 (16174) hydrogen bonds : bond 0.04712 / 3.23 ( 621) hydrogen bonds : angle 4.30223 / 3.06 ( 1724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.431 Fit side-chains REVERT: A 58 MET cc_start: 0.9088 (ttp) cc_final: 0.8661 (ttp) REVERT: C 17 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7553 (mtm-85) REVERT: C 232 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7344 (pp20) REVERT: C 257 LEU cc_start: 0.8178 (tt) cc_final: 0.7903 (tp) REVERT: D 23 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8581 (ptm) REVERT: E 31 LYS cc_start: 0.8169 (mtpm) cc_final: 0.7640 (mttt) REVERT: E 33 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7515 (m-40) REVERT: E 244 GLU cc_start: 0.7640 (tt0) cc_final: 0.7312 (tt0) REVERT: E 270 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7455 (mtpt) REVERT: E 289 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5443 (pp20) REVERT: F 72 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: F 103 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7388 (mtp-110) REVERT: F 138 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.5971 (tt) outliers start: 41 outliers final: 21 residues processed: 213 average time/residue: 0.4744 time to fit residues: 110.7284 Evaluate side-chains 207 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN D 10 ASN E 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125699 restraints weight = 12482.840| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.78 r_work: 0.3328 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11766 Z= 0.154 Angle : 0.539 6.792 16174 Z= 0.299 Chirality : 0.042 0.232 1823 Planarity : 0.004 0.044 1879 Dihedral : 18.893 179.667 2095 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.94 % Allowed : 16.42 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1288 helix: 2.22 (0.21), residues: 608 sheet: -0.49 (0.36), residues: 206 loop : -0.48 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 21 TYR 0.008 0.001 TYR E 229 PHE 0.015 0.001 PHE F 263 TRP 0.010 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11766) covalent geometry : angle 0.53855 / 0.30 (16174) hydrogen bonds : bond 0.04655 / 3.20 ( 621) hydrogen bonds : angle 4.27848 / 3.05 ( 1724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.326 Fit side-chains REVERT: A 58 MET cc_start: 0.9113 (ttp) cc_final: 0.8667 (ttp) REVERT: B 302 LEU cc_start: 0.8182 (mt) cc_final: 0.7931 (mm) REVERT: C 17 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7549 (mtm-85) REVERT: C 257 LEU cc_start: 0.8137 (tt) cc_final: 0.7923 (tp) REVERT: D 23 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8580 (ptm) REVERT: E 31 LYS cc_start: 0.8110 (mtpm) cc_final: 0.7660 (mttm) REVERT: E 33 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7538 (m-40) REVERT: E 244 GLU cc_start: 0.7586 (tt0) cc_final: 0.7336 (tt0) REVERT: E 270 LYS cc_start: 0.7717 (mtpp) cc_final: 0.7399 (mtpt) REVERT: E 289 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5468 (pp20) REVERT: F 72 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: F 138 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6049 (tt) REVERT: F 257 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7809 (mt) outliers start: 42 outliers final: 25 residues processed: 207 average time/residue: 0.4952 time to fit residues: 111.9117 Evaluate side-chains 201 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 257 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN C 33 ASN E 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121338 restraints weight = 12527.838| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.76 r_work: 0.3271 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11766 Z= 0.255 Angle : 0.622 6.738 16174 Z= 0.339 Chirality : 0.046 0.233 1823 Planarity : 0.005 0.050 1879 Dihedral : 19.105 179.994 2095 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.13 % Allowed : 17.26 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.23), residues: 1288 helix: 1.98 (0.20), residues: 607 sheet: -0.51 (0.36), residues: 202 loop : -0.63 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 21 TYR 0.018 0.002 TYR F 223 PHE 0.016 0.002 PHE F 263 TRP 0.010 0.002 TRP B 296 HIS 0.012 0.002 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (11766) covalent geometry : angle 0.62208 / 0.34 (16174) hydrogen bonds : bond 0.05293 / 3.63 ( 621) hydrogen bonds : angle 4.45419 / 3.20 ( 1724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.466 Fit side-chains REVERT: A 41 GLU cc_start: 0.7807 (tt0) cc_final: 0.7467 (tp30) REVERT: A 58 MET cc_start: 0.9146 (ttp) cc_final: 0.8655 (ttp) REVERT: A 71 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8168 (mt) REVERT: B 302 LEU cc_start: 0.8357 (mt) cc_final: 0.8062 (mm) REVERT: C 17 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7621 (mtm-85) REVERT: C 118 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7650 (ttm-80) REVERT: D 23 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8672 (ptm) REVERT: E 31 LYS cc_start: 0.8174 (mtpm) cc_final: 0.7840 (mtpp) REVERT: E 33 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7475 (m-40) REVERT: E 244 GLU cc_start: 0.7629 (tt0) cc_final: 0.7392 (tt0) REVERT: E 289 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5713 (pp20) REVERT: F 72 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: F 76 ASP cc_start: 0.8202 (t70) cc_final: 0.7971 (t0) REVERT: F 118 ARG cc_start: 0.7631 (mtp-110) cc_final: 0.7429 (mtm110) outliers start: 44 outliers final: 24 residues processed: 205 average time/residue: 0.5508 time to fit residues: 123.1812 Evaluate side-chains 203 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 107 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124378 restraints weight = 12405.384| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.75 r_work: 0.3314 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11766 Z= 0.151 Angle : 0.551 7.775 16174 Z= 0.304 Chirality : 0.043 0.240 1823 Planarity : 0.004 0.048 1879 Dihedral : 19.044 179.860 2095 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.28 % Allowed : 18.11 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 606 sheet: -0.63 (0.35), residues: 212 loop : -0.52 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 21 TYR 0.017 0.001 TYR F 223 PHE 0.011 0.001 PHE F 263 TRP 0.011 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11766) covalent geometry : angle 0.55124 / 0.30 (16174) hydrogen bonds : bond 0.04705 / 3.20 ( 621) hydrogen bonds : angle 4.31106 / 3.08 ( 1724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.394 Fit side-chains REVERT: A 58 MET cc_start: 0.9112 (ttp) cc_final: 0.8614 (ttp) REVERT: B 302 LEU cc_start: 0.8256 (mt) cc_final: 0.8025 (mm) REVERT: C 17 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7566 (mtm-85) REVERT: D 23 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8520 (ptm) REVERT: E 31 LYS cc_start: 0.8135 (mtpm) cc_final: 0.7831 (mtpp) REVERT: E 33 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7489 (m-40) REVERT: E 244 GLU cc_start: 0.7600 (tt0) cc_final: 0.7359 (tt0) REVERT: E 289 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5530 (pp20) REVERT: F 72 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: F 118 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7185 (mtp85) outliers start: 35 outliers final: 24 residues processed: 200 average time/residue: 0.4951 time to fit residues: 107.6061 Evaluate side-chains 204 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127066 restraints weight = 12217.635| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.73 r_work: 0.3318 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11766 Z= 0.142 Angle : 0.545 7.427 16174 Z= 0.301 Chirality : 0.042 0.235 1823 Planarity : 0.004 0.039 1879 Dihedral : 18.958 179.935 2095 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.10 % Allowed : 18.95 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1288 helix: 2.16 (0.21), residues: 606 sheet: -0.43 (0.35), residues: 212 loop : -0.54 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 150 TYR 0.017 0.001 TYR F 223 PHE 0.010 0.001 PHE F 263 TRP 0.011 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11766) covalent geometry : angle 0.54466 / 0.30 (16174) hydrogen bonds : bond 0.04574 / 3.12 ( 621) hydrogen bonds : angle 4.27625 / 3.04 ( 1724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.400 Fit side-chains REVERT: A 58 MET cc_start: 0.9111 (ttp) cc_final: 0.8623 (ttp) REVERT: B 33 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8104 (m-40) REVERT: B 302 LEU cc_start: 0.8245 (mt) cc_final: 0.8019 (mm) REVERT: C 17 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7581 (mtm-85) REVERT: D 23 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8537 (ptm) REVERT: E 33 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7495 (m-40) REVERT: E 244 GLU cc_start: 0.7604 (tt0) cc_final: 0.7364 (tt0) REVERT: E 289 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5493 (pp20) REVERT: F 72 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7737 (tt0) outliers start: 33 outliers final: 24 residues processed: 210 average time/residue: 0.5031 time to fit residues: 114.8536 Evaluate side-chains 207 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS F 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126668 restraints weight = 12359.385| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.75 r_work: 0.3330 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11766 Z= 0.148 Angle : 0.560 7.932 16174 Z= 0.308 Chirality : 0.042 0.236 1823 Planarity : 0.004 0.042 1879 Dihedral : 18.946 179.583 2095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.81 % Allowed : 19.70 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1288 helix: 2.16 (0.21), residues: 606 sheet: -0.41 (0.35), residues: 212 loop : -0.55 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 260 TYR 0.016 0.001 TYR F 223 PHE 0.010 0.001 PHE F 263 TRP 0.011 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (11766) covalent geometry : angle 0.55996 / 0.31 (16174) hydrogen bonds : bond 0.04558 / 3.11 ( 621) hydrogen bonds : angle 4.26426 / 3.04 ( 1724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.299 Fit side-chains REVERT: A 58 MET cc_start: 0.9107 (ttp) cc_final: 0.8623 (ttp) REVERT: B 33 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8099 (m-40) REVERT: B 172 ASN cc_start: 0.8767 (t0) cc_final: 0.8415 (t0) REVERT: B 302 LEU cc_start: 0.8255 (mt) cc_final: 0.8024 (mm) REVERT: C 17 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7575 (mtm-85) REVERT: D 23 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8533 (ptm) REVERT: E 31 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7745 (mttp) REVERT: E 33 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7486 (m-40) REVERT: E 244 GLU cc_start: 0.7502 (tt0) cc_final: 0.7230 (tt0) REVERT: E 289 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5547 (pp20) REVERT: E 291 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6889 (tt0) REVERT: F 72 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7760 (tt0) outliers start: 30 outliers final: 23 residues processed: 205 average time/residue: 0.4634 time to fit residues: 103.4955 Evaluate side-chains 208 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123506 restraints weight = 12413.731| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.73 r_work: 0.3299 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11766 Z= 0.193 Angle : 0.590 7.664 16174 Z= 0.323 Chirality : 0.044 0.238 1823 Planarity : 0.004 0.063 1879 Dihedral : 19.047 179.511 2095 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.28 % Allowed : 19.70 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1288 helix: 2.06 (0.21), residues: 605 sheet: -0.58 (0.35), residues: 217 loop : -0.56 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 103 TYR 0.017 0.002 TYR F 223 PHE 0.011 0.001 PHE D 89 TRP 0.010 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (11766) covalent geometry : angle 0.59027 / 0.32 (16174) hydrogen bonds : bond 0.04796 / 3.28 ( 621) hydrogen bonds : angle 4.34449 / 3.10 ( 1724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.88 seconds wall clock time: 65 minutes 20.73 seconds (3920.73 seconds total)